Research workbench
X-ray crystal structure of an O-methyltransferase from anaplasma phagocytophilum bound to SAM and a manganese ion.
Analyse X-ray crystal structure of an O-methyltransferase from anaplasma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PCL
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-methyltransferase family protein
- UniProt
- S6G476
- Ligands
- SAM, MN
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | O-methyltransferase family protein | protein | 213 | 47% helix, 20% strand | S6G476 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.55 | 0.78 | 31 | empty |
| 2 | 182 | 0.51 | 0.78 | 30 | SAM |
| 3 | 177 | 0.51 | 0.78 | 26 | SAM |
| 4 | 84 | 0.32 | 0.74 | 24 | EDO |
| 5 | 52 | 0.25 | 0.73 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 293 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4PCL · X-ray crystal structure of an O-methyltransferase from Anaplasma phagocytophilum bound to… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt S6G476
- Elsewhere: RCSB PDB 4PCL · PDBe 4PCL · UniProt S6G476
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